Posted
by
timothy
on Thursday June 19, 2014 @10:28AM
from the arts-and-science-vs-arts-and-sausages dept.

ciaran_o_riordan (662132) writes The US Supreme Court has just invalidated a patent for being a software patent! To no fanfare, the Court has spent the past months reviewing a case, Alice v. CLS Bank, which posed the question of "Whether claims to computer-implemented inventions ... are directed to patent-eligible subject matter." Their ruling was just published, and what we can say already is that the court was unanimous in finding this particular software patent invalid, saying: "the method claims, which merely require generic computer implementation, fail to transform that abstract idea into a patent-eligible invention," and go on to conclude that because "petitioner's system and media claims add nothing of substance to the underlying abstract idea, we hold that they too are patent ineligible." The End Software Patents wiki has a page for commenting the key extracts and listing third-party analyses. Analysis will appear there as the day(s) goes on. Careful reading is needed to get an idea of what is clearly invalidated (file formats?), and what areas are left for future rulings. If you can help, well, it's a wiki. Software Freedom Law Center's website will also be worth checking in the near future.

I think everyone else was paralyzed with the shock of seeing such "blinding common sense" come from a government institution. You were the first person to recover from the shock, so you get first post.

WASHINGTON—The U.S. Supreme Court on Thursday ruled taxpayers aren't automatically entitled to court hearings to question the motives behind a summons issued by the Internal Revenue Service. The decision was a win for the government, which argued a lower-court ruling made it too easy for taxpayers to obtain court hearings to examine IRS motivations for seeking detailed taxpayer information.

It's not so simple either way, it's more nuanced. They provided a clarification of the rules to be applied:

In an extremely brief and unanimous opinion by Justice Elena Kagan, the Court held that a taxpayer who wants to question Internal Revenue Service (IRS) agents about their motives for issuing a summons may do so if he can point to "specific facts or circumstances plausibly raising an inference of bad faith."... it "will ensure inquiry where the facts and circumstances make inquiry appropriate, without turning every summons dispute into a fishing expedition for official wrongdoing."

The nicest thing about the legal system of the US is that incorporates more nuance each step of the way.

Representatives pass a popular, mostly well intentioned bill, with loads of simplifications.(oh but also lobbyist interests)The executive enforces that with experts who try to apply that stricture in a way that seems reasonable for the pragmatic situation.(Oh but also lobbyist interests)The courts then examine iffy situations and issue precedence on places where that goes too far as well.(oh, but also lob

The one thing that stands out is that software is a Copywrite issue. A machine that already has the mechanics built into it is patenable by its inventor. It makes no sense that a 3rd party can step in and claim a new squence of switching is pattenable. Why? Because the squence ALREADY EXISTED, and N-Factorial other squences exist also.

That's an awful argument. By that definition nothing can ever be copyrighted (which may be your point). Music is, after all, just a unique set of sounds the instruments could already make - the already existed.

I think you fundamentally misunderstood his statement, thought the random throwaway statement at the beginning about software being covered by copyright didn't help.

He talked about how someone could build a machine with mechanisms (triggered by switches) built into it and patent that machine. But once that machine was invented, nobody else should be able to come along and patent using the machine with a certain set of switches on or off, because the switches and their options were already included in the o

I think you fundamentally misunderstood his statement, thought the random throwaway statement at the beginning about software being covered by copyright didn't help.

He talked about how someone could build a machine with mechanisms (triggered by switches) built into it and patent that machine. But once that machine was invented, nobody else should be able to come along and patent using the machine with a certain set of switches on or off, because the switches and their options were already included in the original invention.

The issue of patentability doesn't presume that when someone patents a device, all possible uses of the device are implicitly covered. Its not true that once someone patents the computer, all possible uses for the computer are no longer patentable. The question is one of novelty. If someone tries to patent an invention that involves using another machine with a certain configuration, in the simple case that would almost certainly fail the novelty test, in that the machine was being used in exactly the wa

I wonder if this ought to invalidate crap like the infamous Amazon one-click patent. After all it was also just a generic software implementation of a long-established system, namely storing someone's payment and address details for use with future purchases.

I worry that the stupid FAT32 patent will still be around (since it deals with how a HDD is formatted),

The fact that you can format a RAMDISK or an image file as FAT32; shows that the FAT filesystem actually an abstraction and claims about the abstract mathematical datastructures and parameters of the FAT filesystem really have nothing to do directly with the way the disk (or 'block' device) is formatted.

I wonder if this ought to invalidate crap like the infamous Amazon one-click patent.

Unfortunately, you have to (1) be sued by Amazon for violating the patent (else you have no standing to challenge it), and (2) pay the expense of multi-year court battles with practically no hope of recouping your costs even if you win.

OTOH, I actually like the one-click patent even though I think it's a stupid and invalid patent. It prevents other online stores from putting in a button which can cause you to instantly buy something if you accidentally click it (this has happened to me on Amazon).

Unfortunately, you have to (1) be sued by Amazon for violating the patent (else you have no standing to challenge it)

If your business was damaged by their enforcement activities in the past, regarding their claims about their patent -- such as cease and decist letters, or you were required to license the patent, OR you had an offer to license the patent and refused to license the patent [jdsupra.com], you might also have standing to pursue declaratory judgement.

As far as we know; Amazon took action against Barnes and Noble once, and hasn't sued anyone since, so this isn't likely.

I wonder if this ought to invalidate crap like the infamous Amazon one-click patent. After all it was also just a generic software implementation of a long-established system, namely storing someone's payment and address details for use with future purchases.

I don't think so. My read of the opinion is that what the court found to be lacking in the Alice patents was specificity of invention. In other words, the patent claimed the idea of doing something, but not an actual specific implementation of doing something; the actual invention itself. The court held that you cannot patent an idea, and just saying in the patent application "a computer that implements the idea" is not enough. You have to be very specific and claim something that is not obvious and automatic. Its possible Amazon's one-click patent is sufficiently specific that its still patentable. But what might happen is that Amazon could lose the ability to challenge all forms of one-click, and could only protect its own very specific implementation of it. Its possible the *idea* of one-click purchase could be held unpatentable, and open the door to non-trivial alternate implementations of the same idea. For example, the Amazon patent specifies pre-registering payment information and assigning the customer a unique identifier than binds their electronic shopping cart with that payment information, such that using a single HTML button the purchase can be executed by referencing the payment information bound to the shopping cart's identification number. A one-click system that didn't specifically do that, but say used a single sign-on system that simultaneously authenticated against the payment database and the shopping cart system and triggered a third system to perform the payment process with both systems could be theoretically held to be a different invention to implement the same (unpatentable on its own) idea.

I don't think the ruling directly invalidates the idea of a software patent. But I could see it limiting the claims of software patents enough to allow people to work around them more reasonably, by only requiring software implementers avoid using the exact, precise methods claimed within a patent, and not the entire idea the software patent implements.

I think it will. Reading it, it seems to at the very least (IANAL so I have no idea how far it goes) it will nuke all of the "...with a computer!!" bullshit patents. I hope it goes much farther than that, but even if it doesn't it's a win.

It's hard to say. On the surface though it seems to at least invalidate one large class of software patents. That is, taking an existing idea and then doing it in software is not enough to make a new patentable idea. Which is exactly what so many companies encourage their employees to do when coming up with patents for the portfolio, and similar concept about reusing old ideas with new touch up paint.

For example I was once at a company that did ultrasound imaging, and we had been encouraged in the software group to apply for more patents. One manager said that it could be ok to just take an idea and add "in ultrasound" to the end of it. The example was from a competitor which held the patent for "field upgradable software... in ultrasound", and the patent actually had drawings of an optical disk being delivered via airplane to a remote location and being inserted into a machine.

That points out the big problem really: all these companies feel the need to create all the patents because all of their competitors are doing it. If you're the only company in the field that has to pay licensing fees while everyone else is cross licensing instead, then you're at a serious disadvantage. It's a bit like working in a corrupt country, you feel a bit dirty about paying bribes but maybe you have no choice if you want to do business there.

This ruling extends the basic rule of Bilski that you can't patent an idea to the computer. Essentially, Alice Corp. states that you can't patent a general idea simply by appending the term "on a computer." What the case doesn't say is that all software patents are invalidated. Rather, the software has to be more than just a generic business idea expressed "on a computer."

Alice Corp. was the assignee of several patents for mitigating "settlement risk" via software. Software claims in patent law usually occur in two parts: a method of performing the claimed function and a system for performing the prior claimed method. This basically lets a patent holder guard against people manipulating their way around the system or method claims to perform the exact same function, such as by using a remote server instead of a local hard drive, or querying before step A as opposed to after step A. Alice Corp. had both a system and method patent for mitigating settlement risk. Specifically, the claim contemplated two parties using a third-party intermediary, in this case a computer, to create account ledgers (or "shadow accounts," as the patent called them) based on the accounts of both primary parties, determining available versus unavailable funds, calculating a risk for a given set of transactions, and then issuing instructions to the parties telling them what transactions are permitted and what transactions are too risky to engage in.

The patent itself was to "facilitate the exchange of financial obligations between two parties by using a computer system as a third-party intermediary." If this sounds like an abstract business method, that's because it is. Alice Corp.'s patent was basically a claim to mitigating settlement risk by employing a third party on a computer. The intermediary was just the computer in this case. The district court found that the patent was too vague, because it really only contemplated an idea. The Federal Court on first hearing reversed, saying that it wasn't "manifestly evident" that the patent ideas were abstract, so the case should be litigated rather than dismissed on summary judgment. On second hearing en banc (i.e. with all the Federal Circuit judges present, the Federal Circuit changed its position and determined that the method claims were invalid. There was some internal dispute, however, as to whether the system claims -- i.e. a claim over a computer that performs the function -- was valid.

The Supreme Court determined, in an opinion written by Justice Thomas, that both the method and system claims were abstract and therefore invalid. The rule under a cased called Mayo Collaborative Services v. Promethius Labs requires that an abstract idea, to be patentable, must have some practically beneficial application to either the computer system implementing it or to some other kind of technology. For example, it might be common knowledge that plucking a guitar string emanates a harmonic frequency, so I can't patent plucking a guitar string, but if I find a new, beneficial use for plucking a guitar string, such as a patent on plucking guitar strings to encourage the growth and development of plants (yes, it's nonsensical -- I can't invent good, patentable things on the spot!), then I could patent that. Here, though, the court asked "whether the claims at issue here do more than simply instruct the practitioner to implement the abstract idea of intermediated settlement in a generic computer." Laconically, the Court concluded, "They do not."

So what does this mean for software patents? Well they still are valid as more than just math. Though the Court didn't address the issue directly, it has been generally held that software is sufficiently transformative to warrant patentability. While not a favorite opinion here on Slashdot, that's not altogether nonsensical; if software is sufficiently artistic enough to be copyrightable, then it stands to reason that it has been sufficiently transformed from some

IANAL, but I am a software developer. One additional piece of the puzzle is that Thomas was very careful to use the term 'generic computer'. I.E. the system claims are invalid because the computer implementation at each step of the process does not need anything more than industry standard hardware, common APIs and algorithms/processes common and well known to the industry. Because the computer portion itself could be considered generic, it didn't make the unpatentable idea into a patentable process. That decision left the door open for software patents that require either specialized hardware, or truly novel algorithms not generally known to the industry to implement an otherwise unpatentable idea.

IANAL either, but I suspect there's a bit more to the word "generic" than merely commodity hardware. My understanding is that a generic computer is one that can be programmed to virtually do any task. So any software that runs on a CPU (or even a GPU these days) would be running on a generic computer, but hard drive firmware would not.

This reading would be more in line with some of the other cases, as it means that software by itself cannot be patented, but software that's tied to specific hardware and is s

For example, in the fine article [ipwatchdog.com]
you linked to, Gene Quinn says:

Software can be described by reference to a series of physical
actions operating through gates. This type of micro level
description of what happens is going to be required, [...]

This is BS. Software that can run on different architectures
cannot be described in terms of the physical hardware
the software runs on. At best the patent that resulted would
only be valid on the specific hardware that was described.
I grant you, Microsoft (IIRC) did argue this nonsense
successfully in a courtroom once but just because they were able
to buffalo some lawyers and judges, that doesn't make it true.

But slide to unlock is a physical implementation. Whether or not slide to unlock patents should be invalidated for other reasons they're not strictly software patents, i.e., something that works with a "generic computer implementation".

The two things that can make slide to unlock physical are the rough specifics of the action (size of slider, size of track, visual/tactile feedback, etc) or the specific code approach used to implement it. In each completely separate case the process patented would have to be novel. The notion of a specifically designed sliding motion to unlock the phone probably was novel - the research that went into coming up with a method that was natural and yet almost impossible to happen unintentionally was not ins

A unanimous decision, authored by the most conservative voice on the court (Thomas) with a concurring opinion by one of the most liberal (Sotomayor). If this were the beginning of April, I would say this story was a prank. Yeah, it doesn't completely kill software patents, but it does seem to mortally wound the "business process + software = patent troll profit" problem that is plaguing software development. This is a good day for the judicial branch. It's a good day for the USA.

He regularly writes opinions. He just doesn't ask questions in oral arguments. Much the same as how I lurk and read others comments on Slashdot without asking questions myself, but there is still (often) interesting discussion here.

A few months after SCOTUS or congress shakes things up the USPTO sends out new guidelines to the affected patent examiners. This recently happened for patents involving genes and natural products after last years decision against Myriad (BRCA1 gene patents): examiners were instructed to kick a lot of claims that previously would have been allowed.

I don't think you can blame the examiners for following the guidelines that were in place at the time.

It looks to me like the patent was invalidated because you can't patent an abstract idea. You can't patent the abstract idea of a vehicle with four wheels that uses an internal combustion engine to transport people and cargo. But you can patent the invention of a specific type of automobile, provided that you provide a concrete implementation of that idea by integrating building blocks into a new invention.

Held
: Because the claims are drawn to a patent-ineligible abstract idea,
they are not patent eligible under 101. Pp. 5–17.
(a)
The Court has long held that 101, which defines the subject
matter eligible for patent protecti
on, contains an implicit exception
for ‘
“[l]aws of nature, natural phen
omena, and abstract ideas.’
”
As
-
sociation for Molecular Pathology
v.
Myriad Genetics, Inc.
, 569 U. S.
___, ___. In applying the 101 except
ion, this Court must distinguish
patents that claim the “ ‘buildin[g
] block[s]’ ” of human ingenuity,
which are ineligible for patent prot
ection, from thos
e that integrate the building blocks into something more, see
Mayo Collaborative Ser
-
vices
v.
Prometheus Laboratories, Inc.
, 566 U. S. ___, ___, thereby
“transform[ing]” them into a
patent-eligible invention,
id.,
at ___.
Pp. 5–6."

It was invalidated because the process it describes is super super old. They only thing they added to the old process was using a computer. So if you invent something actually new. Then you can patent that. But "old idea + computer" is not patentable.

It was invalidated because the process it describes is super super old. They only thing they added to the old process was using a computer. So if you invent something actually new. Then you can patent that. But "old idea + computer" is not patentable.

If something's not new, it's invalid under 35 USC 102. If something is obvious, it's invalid under 35 USC 103. Both of these would apply to "old process + computer", and the patent should have been invalidated on those grounds...

But, you have to prove that it's an old idea with some evidence in the form of prior art. And because SCOTUS can't do their own prior art searches, even though they knew it was an old idea, they couldn't invalidate it under 102 or 103... So, instead, they turned to 35 USC 101, and said that this was not a patent eligible method because it was directed to an "abstract idea"... But what's an abstract idea? According to Thomas, anything super super old, like you said. But that's what the other statutes are for.

It's the right outcome - the patent was clearly invalid - but for the wrong reason.

Isn't the definition that you have to be able to give a patent to a developer skilled in the specific art and he/she can implement exactly the device described by the patent without inventing anything new? If that's not possible, the patent is supposed to be invalid because it's an abstract idea instead of a concrete implementation.

Because the district court hearing the case invalidated the patent under section 101, the appeal was limited on those grounds. Neither the appellate court nor the Supreme Court could turn to section 103 (obviousness) to invalidate the patent, because there was no ruling on those grounds at the lower court level for them to review. Now if the respondent had made arguments under section 103 and the district court had ruled the patent to be invalid for obviousness, then

I am willing to bet PJ passively reads Slashdot. If this is so and you read this, we need you back now please. Now more than ever is the clarity of your legal analysis needed. I admit that I am being completely selfish in asking.

So you dont know if it was a man, woman, or machine but you definitively know she was working for IBM, even though she coved more things that had nothing to do with IBM..... I dont think the poster you responded to was the fool in this thread.

While not an expert in this particular case, the holding seems pretty clear - you can't patent an abstract idea and the mere implementation of one does not violate an non-patentable solution. The analysis points out that there is not unique thought or design process involved to protect and the mere following of steps previous outlined does not make something patentable.

Using a computerto create and maintain “shadow” accounts amounts to electronic recordkeeping—one of the most basic functionsof a computer. See, e.g., Benson, 409 U. S., at 65 (noting that a computer “operates . . . upon both new and previously stored data”). The same is true with respect to the use of a computer to obtain data, adjust account balances,and issue automated instructions; all of these computer functions are “well-understood, routine, conventional activit[ies]” previously known to the industry. Mayo, 566
U. S., at ___ (slip op., at 4). In short, each step does nomore than require a generic computer to perform generic computer functions.

I think the above is one of the most important parts of the ruling. Basically stating that your patents stores data, or calculates something won't make it patent elligible if it wasn't patent elligible to start with. You could extend similer thinking to internet patents when talking about "well-understood, routine, convention activiteis"

Given the ubiquity of computers, see 717 F. 3d, at 1286
(Lourie, J., concurring), wholly generic computer imple
-
mentation is not generally the so
rt of “additional featur[e]”
that provides any “practical a
ssurance that the process is
more than a drafting effort designed to monopolize the
[abstract idea] itself.”
Mayo
, 566 U. S., at ___ (slip op., at
8–9).

At least according to Ars [arstechnica.com] this is much less. It's just about killing specific kind of SW patents. Crucially, it still allows patents that "improve the functioning of the computer itself".

I know the headline is correct because Gene Quinn is hopping mad. Quinn makes a living by obtaining software patents and always says he can draft around any limits imposed by the courts, but here's what he's saying today:

"an intellectually bankrupt opinion... will render many hundreds of thousands of software patents completely useless... On first read I donâ(TM)t see how any software patent claims written as method or systems claims can survive challenge."

The quotes sure make it seem like the patent was invalidated for being one of those patents which is nothing more than a wish list of features, with no specific information as to an actual implementation. In other words, a marketing description masquerading as an invention.

I've long thought that so many patents of the past 20 years were like this, especially software patents, and that invalidating these would be a great first step, even if we don't manage to get rid of software patents. So, although it seem

As long as you understand where he's coming from, and that he's been paid as a lawyer to advocate in the past for clients, his stuff is worth reading. His arguments may be biased towards a specific perspective, but they are well-reasoned and documented in support of his position. That's a lot better than the normal bovine effluent you read from tech reporters or (other...) paid shills.

Even PJ would pick-and-choose references to support a position, that's what "making an argument" is all about.

The Supreme Court has held that "abstract ideas" can't be patented, but then has deliberately refrained from defining what an "abstract idea" is!

In the latest Alice decision, they write: "In any event, we need not labor to delimit the precisecontours of the “abstract ideas” category in this case. It is enough to recognize that there is no meaningful distinction between the concept of risk hedging in Bilski and the concept of intermediated settlement at issue here. Both are squarely within the realm of “abstract ideas” as we have used that term."

You're aware that not everything can be defined, right? Even in mathematics, sets are not defined. If there was something used to define what a set is, we would need a definition of whatever that thing is, ad infinitum. A dictionary always give definitions of words in terms of other words. You have to understand what some subset of words in a particular language means before you can use a dictionary for that language.

The concept of an "abstract idea" is something the Supreme Court invented (did I really use that word?) --- to find a way to invalidate obvious patents under section 101. An abstract idea is some knowledge known in the art prior to the invention, applied to a general-purpose machine or computer. That renders the combination of the abstract idea and the application on a computer obvious, if somebody can find a stated motivation in the art from which a rejection can be made.

... Supreme Court has upheld the patentability of software concepts, while setting limits: Companies can't patent a mere abstract idea on a computer, but can patent software ideas that advance or improve upon existing ideas.

The old-school problem with software patents was patenting everything "on a computer". A known eigenvector transform to separate out sinusoid frequencies from a set of sample points would be written and patented "on a computer", because nobody had ever done it in software before.

People started calling method patents "software patents" at some point. That is to say: people would come up with a brilliant new way to analyze and encode data (i.e. compression, psychoacoustics), and folks would start scream

So as I understand what you wrote: Method patents where the method itself is novel are fine, but "on a computer" is not an inventive step if the way to translate an otherwise non-novel method to a computer is obvious to one skilled in the art. Am I right?

Software just feeds a similar list of steps (mathematical transformations) into a computer and does something.

That'd be just fine IMO. Most software patents show vague pictures of the inputs and outputs of those transformations, and then claim to have patented the transformations themselves. Its as if the cotton gin patent simply showed cotton growing in fields, then t-shirts, and had a large box in between them that was patented under "a method for transforming cotton from its natural state," which was then used to attack the loom.

That would actually be fine, if nobody had ever thought to turn fiber into clothing. Once the broad "fiber becomes clothing" patents wear out, you have to look for ways people have made thread before. "PLANT fiber becomes clothing." "Novel way to process Flax and Hemp fiber into clothing by hybrid chemical wash and bacterial fermentation." "New method and device for spinning fibers into clothing." "New method and device for separating high-quality fibers from weak, short fibers to produce better threa

What you're describing is lack of "enablement". A patent is supposed to teach the invention such that one of ordinary skill in the art can make and use the invention.

The problem here is that most patent examiners haven't been engineers, and they're lousy at rejecting the claims you describe because they don't have a reference level of what "ordinary skill" is. If patent examiners were paid more (which might require higher filing fees), we might reach better quality patents.

People started calling method patents "software patents" at some point. That is to say: people would come up with a brilliant new way to analyze and encode data (i.e. compression, psychoacoustics), and folks would start screaming that it shouldn't be patented.

If you come up with a new compression algorithm which is much better than any previous compression algorithm conceived so far, and you can explain how it is so, then it's not a generic idea; it is this complicated non-trivial algorithm you have come

"Hardware patents are really the same way: a system of gears, levers, and cams placed in a certain order create a pair of timed shuttles that can weave fabric at high speeds."Sure. And the way patents were applied to physical machines, what you just mentioned is not patentable, while (at least before today) courts kept ruling the computer equivalent was.

There is no patent controlling high speed mechanical weaving machines. There are a number of patents on high speed mechanical weaving, but they tend toward

So, that leaves something like 1-Click subject to patent claims as a "business method", but according to the above ruling, there is an argument that it lacks sufficient substance as a method to be patentable.

Thus, someone needs to attack "business method" patents and obtain a similar ruling.

This is an extension of the argument that "$process on a computer" is not patentable separately from $process. A previous ruling said that if $process was already patented, "$process on a computer" did not constitute a new patent. This ruling says that if $process is not defined specifically enough to be patented, then "$process on a computer" does not add enough specifics to make the whole process pa

You mean similar like the store charge accounts before everything became a chain? People would go in, pick what they wanted, a clerk would write it down, then the items would be pulled, charged to your account, and delivered to your door by some highschool kid looking for extra money- often by the end of the day.

The concept of one click is not new. Its just a return of yesteryear to todays stores.

Most Supreme Court decisions are unanimous. In the last term, 52% of decisions were 9-0. Another 12% were 8-1.

The decisions are not a closed ballot vote; this is not a test question, where each judge is asked to come up with their answer in private, without knowledge of the other judges' choice. The judges can discuss amongst themselves, weigh the matter, and come to their conclusion.

It will of course wind up being unanimous, unless there is pretty strong disagreement.

Rehnquist wrote a very interesting book The Supreme Court that not only talks about the history of the court and some of its important cases (he did not include any cases that were decided by any judges that he served with), but he also described very nicely the day-to-day workings of a case moving through the system. I found it to be very interesting reading.

FYI -- they discuss the issue of "applying it on a computer" quite a bit throughout the entire opinion, so for all intents and purposes they are discussing a software patent. IANAL; however, previously discussing this with several friends that are, they viewed it as a software patent case too.

Honestly, I'm no fan of software patents, but that's as silly as claiming that if you weren't advancing the art of blacksmithing that you couldn't patent a complex and novel piece of machinery made out of iron.

It is not remotely like that. You can form new things by blacksmiths, you are not limited by the art itself. In programming in a particular language you are 100% limited by the constructs of that language.

Honestly, I'm no fan of software patents, but that's as silly as claiming that if you weren't advancing the art of blacksmithing that you couldn't patent a complex and novel piece of machinery made out of iron.

I disagree. He should be able to publish all the code he wants, and even distribute books and copies of the source code to end users. Patents aren't allowed to restrict speech.

On the other hand: the instant someone takes that bit of code and tells the computer to run it, or ships an appl

If I can use an existing software language to implement your 'patented' idea, then you shouldn't be able to patent that idea.

You can't patent an idea in the first place. Now if you can implement my idea just by being your job as a competent software developer, then the idea + software cannot be patented. But if there is some part of my idea that not every competent developer can do, that requires a non-obvious invention, then the product might be patentable.

I mean, the stupid Arithmetic Coding patent is what killed bzip and replaced it with the less compact bzip2 using Huffman coding.

But then Arithmetic Coding _is_ very clever and the average programmer wouldn't have been able to come up with it. The average programmer wouldn't even be able to understand it, after it is explained to them. Huffman isn't _that_ easy either, but definitely easier. So I would not call this a "stupid" patent.

Since cryptographic and compression algorithms are mathematical in nature, would the "on a computer" apply to them so any cryptographic and compression related patent is invalid?

You are looking at it from the wrong point of view. Here is an unpatentable idea: "We take messages, mash them up in a way so that only the intended receiver can put them back together, and then the intended receiver turns it back into the original message, while anybody else can't read it". No patent. In this case, there is a huge gap between the idea and actually making it work. If that gap is big enough and solving the problem is not obvious and therefore inventive, then it can be patented. And that's the case here. Cryptography and compression can be patented.

The patent that this thread was about was an idea, and an implementation that didn't require any inventive step. No patent.